(edited for length)
I'm seeing sharp edges when I use the Color Fill tool over multiple layers, regardless of the Smooth Edges setting.
To reproduce (Pixelmator Pro 1.0.9 on macOS 10.13.3 on MacBook (Retina, 12-inch, Early 2015)):
Create a 20px × 20px image (it can be bigger but you want to be able to see individual pixels).
Draw a soft black blob on a white background.
Create a new layer.
Select the Color Fill tool and a nice, bright colour.
Ensure that Sample All Layers and Smooth Edges are checked.
On the new layer try to fill the black blob in the bright colour using the Color Fill tool.
Notice that, as you drag the mouse to increase the tolerance that the edge of the fill is soft, as expected.
Release the mouse and notice that the soft edges unexpectedly disappear.
I hope you can reproduce this.
Is something not working like it should? Let us know.